BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081134.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,941,346 number of mapped reads = 1,718,740 (88.53%) number of supplementary alignments = 13,945 (0.72%) number of secondary alignments = 0 number of mapped bases = 114,066,735 bp number of sequenced bases = 114,025,103 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,374 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0714 >>>>>>> ACTG content number of A's = 31,891,047 bp (27.97%) number of C's = 21,135,893 bp (18.54%) number of T's = 35,677,555 bp (31.29%) number of G's = 25,286,910 bp (22.18%) number of N's = 33,698 bp (0.03%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 953,602 number of insertions = 8,948 mapped reads with insertion percentage = 0.52% number of deletions = 25,986 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3117X There is a 3.26% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9354428 0.037530209403169354 0.5268525088119862 chr2 243199373 9623315 0.03956965382472429 0.3910487298900091 chr3 198022430 7968936 0.04024259272043071 0.21975078919433927 chr4 191154276 7419552 0.03881447046468372 0.22480277099464085 chr5 180915260 7172140 0.039643643106723005 0.2197233317521759 chr6 171115067 6968058 0.040721475450201 0.29147654675129114 chr7 159138663 5644227 0.03546735214182364 0.35156873294331104 chr8 146364022 6289944 0.04297465944192214 0.3846833125967146 chr9 141213431 4975724 0.03523548691342256 0.28760177522068875 chr10 135534747 5365174 0.03958522901879914 0.2805045407683419 chr11 135006516 4691535 0.034750433823505227 0.2755906952231121 chr12 133851895 4469613 0.03339222802934542 0.20327792014808482 chr13 115169878 3945167 0.03425519822118766 0.20209751593313544 chr14 107349540 3588476 0.033427958797028846 0.21288371859519853 chr15 102531392 3483866 0.03397853020468112 0.20653554781489397 chr16 90354753 2497126 0.02763690804400738 0.20904314024696088 chr17 81195210 3189760 0.0392850760531317 0.24687898570033948 chr18 78077248 2901847 0.03716635862985335 0.5495870279219156 chr19 59128983 2324256 0.03930823569213088 0.3828139261550421 chr20 63025520 2366502 0.03754831376242512 0.21819700540653275 chr21 48129895 1484639 0.030846504028317536 0.20634682954055905 chr22 51304566 1291795 0.025178948010202446 0.17268289297747264 chrMT 16571 1147 0.06921730734415545 0.33714822339055633 chrX 155270560 6769900 0.043600667119381806 0.2559207116442992 chrY 59373566 279608 0.004709301105478489 0.09940693122203446